Foundations#
Welcome to the Foundations of MolSysMT. This section introduces the core principles, architectural invariants, and high-performance design that enable MolSysMT to operate seamlessly across different molecular structures, file formats, and computational tools.
Rather than treating molecular systems as rigid data structures bound to a specific software package, MolSysMT builds a form-agnostic bridge. Here you will learn how systems are defined, how physical units and quantities are safely enforced, how selection syntaxes are interpreted, and how native representations ensure speed and interoperability across the structural biology ecosystem. Explore the 8 pillars below to master the underlying framework.
Sections#
Mission, installation, documentation navigation, toolbox overview, and demo systems.
Universal definition of molecular systems, forms, items, elements, and physical attributes.
Native object classes, topology data, H5MSM trajectory storage, and file handlers.
Syntactic modes, declarative selection queries, and core API function patterns.
Zero-copy array views, chunked execution for large trajectories, and Rust acceleration.
Physical units, ArgDigest boundary safety, DepDigest lazy loading, and SMonitor diagnostics.
Compatibility matrix across data forms, physical-chemical scales, syntaxes, and bridges.
MolSysSuite overview, biophysics tools, and developer software engineering infrastructure.